# DeeDeeExperiment: An S4 Class for managing and exploring omics analysis results

## Documentation for package ‘DeeDeeExperiment’ version 1.2.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

DeeDeeExperiment-package | DeeDeeExperiment
.DeeDeeExperiment | The DeeDeeExperiment class
addDEA | Methods for DeeDeeExperiment objects
addDEA-method | Methods for DeeDeeExperiment objects
addFEA | Methods for DeeDeeExperiment objects
addFEA-method | Methods for DeeDeeExperiment objects
addScenarioInfo | Methods for DeeDeeExperiment objects
addScenarioInfo-method | Methods for DeeDeeExperiment objects
clusterPro_res | 'clusterPro_res'
dd_list_original | dd_list_original
DeeDeeExperiment | The DeeDeeExperiment class
DeeDeeExperiment-class | The DeeDeeExperiment class
DeeDeeExperiment-methods | Methods for DeeDeeExperiment objects
DeeDeeExperiment-misc | Miscellaneous DeeDeeExperiment methods
DeeDeeExperiment-pkg | DeeDeeExperiment
de_limma | A sample 'MArrayLM' object
de_named_list | de_named_list
dge_exact_IFNg_both | A sample 'DGEExact' object
dge_exact_IFNg_naive | A sample 'DGEExact' object
dge_exact_Salm_both | A sample 'DGEExact' object
dge_exact_Salm_naive | A sample 'DGEExact' object
dge_lrt_IFNg_both | A sample 'DGELRT' object
dge_lrt_IFNg_naive | A sample 'DGELRT' object
dge_lrt_Salm_both | A sample 'DGELRT' object
dge_lrt_Salm_naive | A sample 'DGELRT' object
enrichr_res | 'enrichr_res'
export_result_for_dde | Export DEA/FEA/ASSAY results from a 'DeeDeeExperiment' to excel files
fgseaRes | 'fgseaRes'
getDEA | Methods for DeeDeeExperiment objects
getDEA-method | Methods for DeeDeeExperiment objects
getDEAInfo | Methods for DeeDeeExperiment objects
getDEAInfo-method | Methods for DeeDeeExperiment objects
getDEAInfo<- | Methods for DeeDeeExperiment objects
getDEAInfo<--method | Methods for DeeDeeExperiment objects
getDEAList | Methods for DeeDeeExperiment objects
getDEAList-method | Methods for DeeDeeExperiment objects
getDEANames | Methods for DeeDeeExperiment objects
getDEANames-method | Methods for DeeDeeExperiment objects
getFEA | Methods for DeeDeeExperiment objects
getFEA-method | Methods for DeeDeeExperiment objects
getFEAInfo | Methods for DeeDeeExperiment objects
getFEAInfo-method | Methods for DeeDeeExperiment objects
getFEAInfo<- | Methods for DeeDeeExperiment objects
getFEAInfo<--method | Methods for DeeDeeExperiment objects
getFEAList | Methods for DeeDeeExperiment objects
getFEAList-method | Methods for DeeDeeExperiment objects
getFEANames | Methods for DeeDeeExperiment objects
getFEANames-method | Methods for DeeDeeExperiment objects
gost_res | 'gost_res'
gsea_res | 'gsea_res'
IFNg_both | A sample 'DESeqResults' object
IFNg_naive | A sample 'DESeqResults' object
limma_list_for_dde | Convert a 'MArrayLM' object with multiple contrasts into a list of DE results tables compatible with DeeDeeExperiment
linkDEAandFEA | Methods for DeeDeeExperiment objects
linkDEAandFEA-method | Methods for DeeDeeExperiment objects
muscat_list_for_dde | Convert 'muscat::pbDS()' results into a flat list of data frames compatible with 'DeeDeeExperiment'
muscat_res | 'muscat_res'
removeDEA | Methods for DeeDeeExperiment objects
removeDEA-method | Methods for DeeDeeExperiment objects
removeFEA | Methods for DeeDeeExperiment objects
removeFEA-method | Methods for DeeDeeExperiment objects
renameDEA | Methods for DeeDeeExperiment objects
renameDEA-method | Methods for DeeDeeExperiment objects
renameFEA | Methods for DeeDeeExperiment objects
renameFEA-method | Methods for DeeDeeExperiment objects
Salm_both | A sample 'DESeqResults' object
Salm_naive | A sample 'DESeqResults' object
show-method | Miscellaneous DeeDeeExperiment methods
summary-method | Miscellaneous DeeDeeExperiment methods
supported_fea_formats | Display available FEA formats
topGO_results_list | 'topGO_results_list'